Multiple sequence alignment - TraesCS7A01G541900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G541900 chr7A 100.000 2354 0 0 1 2354 718313849 718311496 0.000000e+00 4348.0
1 TraesCS7A01G541900 chr7A 89.174 1053 79 14 616 1665 718208201 718207181 0.000000e+00 1280.0
2 TraesCS7A01G541900 chr7A 83.454 689 75 18 621 1302 718252422 718251766 2.590000e-169 604.0
3 TraesCS7A01G541900 chr7A 78.736 823 125 33 931 1730 718518080 718517285 2.700000e-139 505.0
4 TraesCS7A01G541900 chr7A 96.226 265 8 2 1921 2185 252742474 252742736 1.290000e-117 433.0
5 TraesCS7A01G541900 chr7A 78.797 698 106 29 931 1607 718522983 718522307 4.650000e-117 431.0
6 TraesCS7A01G541900 chr7A 90.909 110 10 0 2233 2342 718206746 718206637 5.240000e-32 148.0
7 TraesCS7A01G541900 chr7A 80.357 112 19 1 1677 1785 718207139 718207028 5.390000e-12 82.4
8 TraesCS7A01G541900 chr7D 90.133 1054 73 15 614 1664 623389979 623391004 0.000000e+00 1341.0
9 TraesCS7A01G541900 chr7D 87.124 1064 77 21 614 1667 623293265 623294278 0.000000e+00 1151.0
10 TraesCS7A01G541900 chr7D 87.030 1064 78 21 614 1667 623283266 623284279 0.000000e+00 1146.0
11 TraesCS7A01G541900 chr7D 76.907 944 128 38 644 1563 623027014 623027891 9.920000e-124 453.0
12 TraesCS7A01G541900 chr7D 96.958 263 6 2 1922 2184 439780777 439780517 7.720000e-120 440.0
13 TraesCS7A01G541900 chr7D 90.411 146 9 4 621 766 623304766 623304906 1.110000e-43 187.0
14 TraesCS7A01G541900 chr7D 80.090 221 30 9 955 1174 622995401 622995608 4.050000e-33 152.0
15 TraesCS7A01G541900 chr7D 78.505 214 28 14 982 1181 623393627 623393836 8.830000e-25 124.0
16 TraesCS7A01G541900 chr7D 94.118 68 4 0 2277 2344 623391508 623391575 1.150000e-18 104.0
17 TraesCS7A01G541900 chr7D 87.671 73 3 1 2288 2354 623341999 623342071 1.940000e-11 80.5
18 TraesCS7A01G541900 chr6A 99.349 614 4 0 1 614 461808201 461808814 0.000000e+00 1112.0
19 TraesCS7A01G541900 chr6A 96.552 232 8 0 392 623 416744268 416744037 3.670000e-103 385.0
20 TraesCS7A01G541900 chr7B 85.856 806 75 22 700 1476 720812647 720811852 0.000000e+00 821.0
21 TraesCS7A01G541900 chr7B 96.212 264 9 1 1922 2185 598954776 598955038 4.650000e-117 431.0
22 TraesCS7A01G541900 chr7B 74.780 567 89 37 898 1437 720932681 720932142 3.070000e-49 206.0
23 TraesCS7A01G541900 chr7B 75.973 437 73 24 934 1361 720948591 720948178 1.850000e-46 196.0
24 TraesCS7A01G541900 chr7B 90.265 113 11 0 2232 2344 720927042 720926930 5.240000e-32 148.0
25 TraesCS7A01G541900 chr3A 95.787 356 14 1 31 385 47037442 47037797 7.300000e-160 573.0
26 TraesCS7A01G541900 chr3B 95.115 348 16 1 39 385 59211246 59211593 4.420000e-152 547.0
27 TraesCS7A01G541900 chr5D 95.588 272 9 3 1923 2192 321547745 321547475 1.290000e-117 433.0
28 TraesCS7A01G541900 chr6D 96.212 264 8 2 1923 2186 26353980 26354241 4.650000e-117 431.0
29 TraesCS7A01G541900 chr6D 95.865 266 9 2 1923 2188 388990881 388990618 1.670000e-116 429.0
30 TraesCS7A01G541900 chr6D 96.957 230 7 0 385 614 266000024 266000253 1.020000e-103 387.0
31 TraesCS7A01G541900 chr2D 96.212 264 9 1 1921 2184 204112682 204112944 4.650000e-117 431.0
32 TraesCS7A01G541900 chr2B 95.238 273 11 2 1914 2186 119319703 119319433 4.650000e-117 431.0
33 TraesCS7A01G541900 chr4D 96.212 264 7 3 1922 2185 349816319 349816059 1.670000e-116 429.0
34 TraesCS7A01G541900 chr4D 96.567 233 8 0 385 617 322665836 322665604 1.020000e-103 387.0
35 TraesCS7A01G541900 chr3D 95.349 258 10 2 130 385 36590538 36590795 2.180000e-110 409.0
36 TraesCS7A01G541900 chr6B 97.391 230 6 0 385 614 653877298 653877069 2.190000e-105 392.0
37 TraesCS7A01G541900 chr6B 96.552 232 8 0 385 616 462629014 462629245 3.670000e-103 385.0
38 TraesCS7A01G541900 chr1D 96.552 232 8 0 385 616 486683098 486683329 3.670000e-103 385.0
39 TraesCS7A01G541900 chr1D 96.137 233 9 0 385 617 59013514 59013282 4.750000e-102 381.0
40 TraesCS7A01G541900 chr5B 96.154 234 9 0 385 618 101252808 101253041 1.320000e-102 383.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G541900 chr7A 718311496 718313849 2353 True 4348.000000 4348 100.000000 1 2354 1 chr7A.!!$R2 2353
1 TraesCS7A01G541900 chr7A 718251766 718252422 656 True 604.000000 604 83.454000 621 1302 1 chr7A.!!$R1 681
2 TraesCS7A01G541900 chr7A 718517285 718518080 795 True 505.000000 505 78.736000 931 1730 1 chr7A.!!$R3 799
3 TraesCS7A01G541900 chr7A 718206637 718208201 1564 True 503.466667 1280 86.813333 616 2342 3 chr7A.!!$R5 1726
4 TraesCS7A01G541900 chr7A 718522307 718522983 676 True 431.000000 431 78.797000 931 1607 1 chr7A.!!$R4 676
5 TraesCS7A01G541900 chr7D 623293265 623294278 1013 False 1151.000000 1151 87.124000 614 1667 1 chr7D.!!$F4 1053
6 TraesCS7A01G541900 chr7D 623283266 623284279 1013 False 1146.000000 1146 87.030000 614 1667 1 chr7D.!!$F3 1053
7 TraesCS7A01G541900 chr7D 623389979 623393836 3857 False 523.000000 1341 87.585333 614 2344 3 chr7D.!!$F7 1730
8 TraesCS7A01G541900 chr7D 623027014 623027891 877 False 453.000000 453 76.907000 644 1563 1 chr7D.!!$F2 919
9 TraesCS7A01G541900 chr6A 461808201 461808814 613 False 1112.000000 1112 99.349000 1 614 1 chr6A.!!$F1 613
10 TraesCS7A01G541900 chr7B 720811852 720812647 795 True 821.000000 821 85.856000 700 1476 1 chr7B.!!$R1 776
11 TraesCS7A01G541900 chr7B 720932142 720932681 539 True 206.000000 206 74.780000 898 1437 1 chr7B.!!$R3 539

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
730 733 0.039472 TCTGCCAGGGCTGCATTAAA 59.961 50.0 12.19 0.0 42.51 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1826 1.066645 CCTAACGGGTAAGGAAACGCT 60.067 52.381 0.0 0.0 34.58 5.07 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 226 4.739716 CACTTTCTTTTGTAATGCAGCGTT 59.260 37.500 4.94 4.94 0.00 4.84
396 397 6.199937 ACTAAGTGGATTGAAATGTGATGC 57.800 37.500 0.00 0.00 0.00 3.91
512 513 4.390264 GCTTTGAGGGTTCTAGTCTTTGT 58.610 43.478 0.00 0.00 0.00 2.83
517 518 4.202749 TGAGGGTTCTAGTCTTTGTCCCTA 60.203 45.833 0.00 0.00 43.04 3.53
709 711 3.845259 GGGCCATGCATGCAGGTG 61.845 66.667 28.58 20.91 0.00 4.00
730 733 0.039472 TCTGCCAGGGCTGCATTAAA 59.961 50.000 12.19 0.00 42.51 1.52
731 734 0.458669 CTGCCAGGGCTGCATTAAAG 59.541 55.000 12.19 0.00 42.51 1.85
732 735 0.039472 TGCCAGGGCTGCATTAAAGA 59.961 50.000 12.19 0.00 42.51 2.52
733 736 1.342275 TGCCAGGGCTGCATTAAAGAT 60.342 47.619 12.19 0.00 42.51 2.40
734 737 1.758862 GCCAGGGCTGCATTAAAGATT 59.241 47.619 2.30 0.00 38.26 2.40
735 738 2.169144 GCCAGGGCTGCATTAAAGATTT 59.831 45.455 2.30 0.00 38.26 2.17
736 739 3.384467 GCCAGGGCTGCATTAAAGATTTA 59.616 43.478 2.30 0.00 38.26 1.40
816 839 0.315251 CTCACCGCAGAGAACTGTCA 59.685 55.000 0.00 0.00 45.04 3.58
844 871 3.500982 CAATTCAATTAGCACCACACCG 58.499 45.455 0.00 0.00 0.00 4.94
894 921 2.362369 CGGTGCCTCCAGGACTCAT 61.362 63.158 0.00 0.00 37.39 2.90
895 922 1.524482 GGTGCCTCCAGGACTCATC 59.476 63.158 0.00 0.00 37.39 2.92
896 923 1.267574 GGTGCCTCCAGGACTCATCA 61.268 60.000 0.00 0.00 37.39 3.07
900 927 1.134551 GCCTCCAGGACTCATCACTTC 60.135 57.143 0.00 0.00 37.39 3.01
907 934 0.992802 GACTCATCACTTCGCCGTTC 59.007 55.000 0.00 0.00 0.00 3.95
920 947 2.280524 CGTTCGTGCTCCCCACAA 60.281 61.111 0.00 0.00 44.91 3.33
927 961 2.159382 CGTGCTCCCCACAATTTAACT 58.841 47.619 0.00 0.00 44.91 2.24
1132 1181 4.373116 GGTTCCTCACCGCGCAGA 62.373 66.667 8.75 0.37 35.12 4.26
1240 1335 1.452651 GCATGGAAGGCTGCTGCTA 60.453 57.895 15.64 0.00 42.67 3.49
1388 1491 5.084818 TCGATCTCTGCTAAAATGGTTGA 57.915 39.130 0.00 0.00 0.00 3.18
1395 1498 2.822561 TGCTAAAATGGTTGATCCGCAA 59.177 40.909 0.00 0.00 39.52 4.85
1423 1528 2.704725 TTCGGTTGTAGGTACGTCAC 57.295 50.000 0.00 0.00 0.00 3.67
1445 1581 2.353406 GGTCTAGCTACTTTGCGTGGAA 60.353 50.000 0.00 0.00 38.13 3.53
1508 1655 3.675790 ATGTGGGCAGGCATGGGT 61.676 61.111 0.00 0.00 0.00 4.51
1525 1673 2.569853 TGGGTTTCATCGGCTCTTCTAA 59.430 45.455 0.00 0.00 0.00 2.10
1526 1674 3.008594 TGGGTTTCATCGGCTCTTCTAAA 59.991 43.478 0.00 0.00 0.00 1.85
1527 1675 4.200092 GGGTTTCATCGGCTCTTCTAAAT 58.800 43.478 0.00 0.00 0.00 1.40
1607 1756 2.532250 AATTCCCAATTTCTCCGGCT 57.468 45.000 0.00 0.00 0.00 5.52
1610 1759 1.580059 TCCCAATTTCTCCGGCTAGT 58.420 50.000 0.00 0.00 0.00 2.57
1619 1770 1.828595 TCTCCGGCTAGTTTGTATGCA 59.171 47.619 0.00 0.00 0.00 3.96
1717 1941 9.606631 AGGAATCTAGAATAAGAACATCACAAC 57.393 33.333 0.00 0.00 0.00 3.32
1725 1949 8.517878 AGAATAAGAACATCACAACAATTGAGG 58.482 33.333 13.59 6.01 0.00 3.86
1731 1955 6.707440 ACATCACAACAATTGAGGTGTTAA 57.293 33.333 23.49 12.26 41.76 2.01
1754 1978 9.715121 TTAATCAACACCGAATAGAAAAGTACT 57.285 29.630 0.00 0.00 0.00 2.73
1755 1979 7.596749 ATCAACACCGAATAGAAAAGTACTG 57.403 36.000 0.00 0.00 0.00 2.74
1759 1986 4.567159 CACCGAATAGAAAAGTACTGCCTC 59.433 45.833 0.00 0.00 0.00 4.70
1760 1987 4.120589 CCGAATAGAAAAGTACTGCCTCC 58.879 47.826 0.00 0.00 0.00 4.30
1764 1991 1.550976 AGAAAAGTACTGCCTCCTCCG 59.449 52.381 0.00 0.00 0.00 4.63
1776 2003 1.797211 CTCCTCCGTTAGGCTAGCCG 61.797 65.000 27.83 15.60 46.10 5.52
1855 2165 9.166173 TCAAATTGTCAATCTAAGGATACACTG 57.834 33.333 0.00 0.00 41.41 3.66
1861 2171 2.679082 TCTAAGGATACACTGAGGCCC 58.321 52.381 0.00 0.00 41.41 5.80
1870 2180 5.010012 GGATACACTGAGGCCCAATAAATTG 59.990 44.000 0.00 0.00 37.52 2.32
1890 2200 6.591750 ATTGGAATGGAGATAGTACTACCG 57.408 41.667 4.31 0.00 0.00 4.02
1926 2236 5.086104 TGAACCTCCAACTGCTTATACTC 57.914 43.478 0.00 0.00 0.00 2.59
1927 2237 4.081087 TGAACCTCCAACTGCTTATACTCC 60.081 45.833 0.00 0.00 0.00 3.85
1928 2238 2.772515 ACCTCCAACTGCTTATACTCCC 59.227 50.000 0.00 0.00 0.00 4.30
1930 2240 3.070302 CCTCCAACTGCTTATACTCCCTC 59.930 52.174 0.00 0.00 0.00 4.30
1931 2241 3.039011 TCCAACTGCTTATACTCCCTCC 58.961 50.000 0.00 0.00 0.00 4.30
1932 2242 2.224066 CCAACTGCTTATACTCCCTCCG 60.224 54.545 0.00 0.00 0.00 4.63
1936 2246 3.132467 ACTGCTTATACTCCCTCCGTTTC 59.868 47.826 0.00 0.00 0.00 2.78
1937 2247 3.371965 TGCTTATACTCCCTCCGTTTCT 58.628 45.455 0.00 0.00 0.00 2.52
1938 2248 3.773119 TGCTTATACTCCCTCCGTTTCTT 59.227 43.478 0.00 0.00 0.00 2.52
1939 2249 4.224370 TGCTTATACTCCCTCCGTTTCTTT 59.776 41.667 0.00 0.00 0.00 2.52
1940 2250 5.183969 GCTTATACTCCCTCCGTTTCTTTT 58.816 41.667 0.00 0.00 0.00 2.27
1941 2251 5.646793 GCTTATACTCCCTCCGTTTCTTTTT 59.353 40.000 0.00 0.00 0.00 1.94
1942 2252 6.820152 GCTTATACTCCCTCCGTTTCTTTTTA 59.180 38.462 0.00 0.00 0.00 1.52
1943 2253 7.201591 GCTTATACTCCCTCCGTTTCTTTTTAC 60.202 40.741 0.00 0.00 0.00 2.01
1944 2254 4.701651 ACTCCCTCCGTTTCTTTTTACT 57.298 40.909 0.00 0.00 0.00 2.24
1945 2255 4.639334 ACTCCCTCCGTTTCTTTTTACTC 58.361 43.478 0.00 0.00 0.00 2.59
1946 2256 4.347292 ACTCCCTCCGTTTCTTTTTACTCT 59.653 41.667 0.00 0.00 0.00 3.24
1947 2257 4.638304 TCCCTCCGTTTCTTTTTACTCTG 58.362 43.478 0.00 0.00 0.00 3.35
1948 2258 3.188667 CCCTCCGTTTCTTTTTACTCTGC 59.811 47.826 0.00 0.00 0.00 4.26
1949 2259 3.813166 CCTCCGTTTCTTTTTACTCTGCA 59.187 43.478 0.00 0.00 0.00 4.41
1950 2260 4.455877 CCTCCGTTTCTTTTTACTCTGCAT 59.544 41.667 0.00 0.00 0.00 3.96
1951 2261 5.642063 CCTCCGTTTCTTTTTACTCTGCATA 59.358 40.000 0.00 0.00 0.00 3.14
1952 2262 6.316390 CCTCCGTTTCTTTTTACTCTGCATAT 59.684 38.462 0.00 0.00 0.00 1.78
1953 2263 7.494625 CCTCCGTTTCTTTTTACTCTGCATATA 59.505 37.037 0.00 0.00 0.00 0.86
1954 2264 8.780846 TCCGTTTCTTTTTACTCTGCATATAA 57.219 30.769 0.00 0.00 0.00 0.98
1955 2265 8.879759 TCCGTTTCTTTTTACTCTGCATATAAG 58.120 33.333 0.00 0.00 0.00 1.73
1956 2266 8.879759 CCGTTTCTTTTTACTCTGCATATAAGA 58.120 33.333 0.00 0.00 0.00 2.10
1964 2274 9.679661 TTTTACTCTGCATATAAGATTTGGTCA 57.320 29.630 0.00 0.00 0.00 4.02
1965 2275 9.679661 TTTACTCTGCATATAAGATTTGGTCAA 57.320 29.630 0.00 0.00 0.00 3.18
1966 2276 9.679661 TTACTCTGCATATAAGATTTGGTCAAA 57.320 29.630 0.00 0.00 34.46 2.69
1967 2277 8.218338 ACTCTGCATATAAGATTTGGTCAAAG 57.782 34.615 2.55 0.00 33.32 2.77
1968 2278 7.831193 ACTCTGCATATAAGATTTGGTCAAAGT 59.169 33.333 2.55 0.00 33.32 2.66
1969 2279 8.213518 TCTGCATATAAGATTTGGTCAAAGTC 57.786 34.615 2.55 1.51 33.32 3.01
1970 2280 7.828717 TCTGCATATAAGATTTGGTCAAAGTCA 59.171 33.333 2.55 0.00 33.32 3.41
1971 2281 8.347004 TGCATATAAGATTTGGTCAAAGTCAA 57.653 30.769 2.55 0.00 33.32 3.18
1972 2282 8.801299 TGCATATAAGATTTGGTCAAAGTCAAA 58.199 29.630 2.55 0.00 37.29 2.69
1973 2283 9.076596 GCATATAAGATTTGGTCAAAGTCAAAC 57.923 33.333 2.55 0.00 35.97 2.93
1977 2287 7.639113 AAGATTTGGTCAAAGTCAAACTACA 57.361 32.000 2.55 0.00 35.97 2.74
1978 2288 7.027778 AGATTTGGTCAAAGTCAAACTACAC 57.972 36.000 2.55 0.00 35.97 2.90
1979 2289 6.601613 AGATTTGGTCAAAGTCAAACTACACA 59.398 34.615 2.55 0.00 35.97 3.72
1980 2290 6.576662 TTTGGTCAAAGTCAAACTACACAA 57.423 33.333 0.00 0.00 0.00 3.33
1981 2291 6.576662 TTGGTCAAAGTCAAACTACACAAA 57.423 33.333 0.00 0.00 0.00 2.83
1982 2292 6.189677 TGGTCAAAGTCAAACTACACAAAG 57.810 37.500 0.00 0.00 0.00 2.77
1983 2293 5.708230 TGGTCAAAGTCAAACTACACAAAGT 59.292 36.000 0.00 0.00 0.00 2.66
1984 2294 6.207810 TGGTCAAAGTCAAACTACACAAAGTT 59.792 34.615 0.00 0.00 41.46 2.66
1995 2305 8.840833 AAACTACACAAAGTTTGACCAAATTT 57.159 26.923 22.23 11.30 45.60 1.82
1996 2306 9.930693 AAACTACACAAAGTTTGACCAAATTTA 57.069 25.926 22.23 0.00 45.60 1.40
2065 2375 7.372634 GAAAATACGTTTCATGATGCATCTG 57.627 36.000 26.32 20.36 44.42 2.90
2066 2376 6.682423 AAATACGTTTCATGATGCATCTGA 57.318 33.333 26.32 22.04 0.00 3.27
2067 2377 6.872628 AATACGTTTCATGATGCATCTGAT 57.127 33.333 26.32 10.77 0.00 2.90
2068 2378 7.967890 AATACGTTTCATGATGCATCTGATA 57.032 32.000 26.32 17.86 0.00 2.15
2069 2379 7.967890 ATACGTTTCATGATGCATCTGATAA 57.032 32.000 26.32 17.90 0.00 1.75
2070 2380 6.872628 ACGTTTCATGATGCATCTGATAAT 57.127 33.333 26.32 9.30 0.00 1.28
2071 2381 7.967890 ACGTTTCATGATGCATCTGATAATA 57.032 32.000 26.32 5.68 0.00 0.98
2072 2382 8.557592 ACGTTTCATGATGCATCTGATAATAT 57.442 30.769 26.32 7.86 0.00 1.28
2073 2383 9.006839 ACGTTTCATGATGCATCTGATAATATT 57.993 29.630 26.32 8.29 0.00 1.28
2074 2384 9.274065 CGTTTCATGATGCATCTGATAATATTG 57.726 33.333 26.32 10.34 0.00 1.90
2135 2445 7.484035 AGTTAGTCAAACTCTACAAAGCTTG 57.516 36.000 0.00 0.00 45.64 4.01
2136 2446 7.272978 AGTTAGTCAAACTCTACAAAGCTTGA 58.727 34.615 0.00 0.00 45.64 3.02
2137 2447 5.993106 AGTCAAACTCTACAAAGCTTGAC 57.007 39.130 0.00 10.63 0.00 3.18
2138 2448 5.675538 AGTCAAACTCTACAAAGCTTGACT 58.324 37.500 13.94 13.94 0.00 3.41
2139 2449 6.116126 AGTCAAACTCTACAAAGCTTGACTT 58.884 36.000 13.94 3.16 41.70 3.01
2149 2459 3.801114 AAGCTTGACTTTGACCAAACC 57.199 42.857 0.00 0.00 33.71 3.27
2150 2460 3.018423 AGCTTGACTTTGACCAAACCT 57.982 42.857 0.00 0.00 0.00 3.50
2151 2461 2.952310 AGCTTGACTTTGACCAAACCTC 59.048 45.455 0.00 0.00 0.00 3.85
2152 2462 2.687935 GCTTGACTTTGACCAAACCTCA 59.312 45.455 0.00 0.00 0.00 3.86
2153 2463 3.319122 GCTTGACTTTGACCAAACCTCAT 59.681 43.478 0.00 0.00 0.00 2.90
2154 2464 4.518970 GCTTGACTTTGACCAAACCTCATA 59.481 41.667 0.00 0.00 0.00 2.15
2155 2465 5.183904 GCTTGACTTTGACCAAACCTCATAT 59.816 40.000 0.00 0.00 0.00 1.78
2156 2466 6.573664 TTGACTTTGACCAAACCTCATATG 57.426 37.500 0.00 0.00 0.00 1.78
2157 2467 4.458989 TGACTTTGACCAAACCTCATATGC 59.541 41.667 0.00 0.00 0.00 3.14
2158 2468 3.440173 ACTTTGACCAAACCTCATATGCG 59.560 43.478 0.00 0.00 0.00 4.73
2159 2469 3.342377 TTGACCAAACCTCATATGCGA 57.658 42.857 0.00 0.00 0.00 5.10
2160 2470 3.342377 TGACCAAACCTCATATGCGAA 57.658 42.857 0.00 0.00 0.00 4.70
2161 2471 3.006940 TGACCAAACCTCATATGCGAAC 58.993 45.455 0.00 0.00 0.00 3.95
2162 2472 3.270877 GACCAAACCTCATATGCGAACT 58.729 45.455 0.00 0.00 0.00 3.01
2163 2473 4.081365 TGACCAAACCTCATATGCGAACTA 60.081 41.667 0.00 0.00 0.00 2.24
2164 2474 4.839121 ACCAAACCTCATATGCGAACTAA 58.161 39.130 0.00 0.00 0.00 2.24
2165 2475 5.250200 ACCAAACCTCATATGCGAACTAAA 58.750 37.500 0.00 0.00 0.00 1.85
2166 2476 5.708230 ACCAAACCTCATATGCGAACTAAAA 59.292 36.000 0.00 0.00 0.00 1.52
2167 2477 6.207810 ACCAAACCTCATATGCGAACTAAAAA 59.792 34.615 0.00 0.00 0.00 1.94
2168 2478 6.747280 CCAAACCTCATATGCGAACTAAAAAG 59.253 38.462 0.00 0.00 0.00 2.27
2169 2479 7.361713 CCAAACCTCATATGCGAACTAAAAAGA 60.362 37.037 0.00 0.00 0.00 2.52
2170 2480 7.681939 AACCTCATATGCGAACTAAAAAGAA 57.318 32.000 0.00 0.00 0.00 2.52
2171 2481 7.681939 ACCTCATATGCGAACTAAAAAGAAA 57.318 32.000 0.00 0.00 0.00 2.52
2172 2482 7.527457 ACCTCATATGCGAACTAAAAAGAAAC 58.473 34.615 0.00 0.00 0.00 2.78
2173 2483 7.174253 ACCTCATATGCGAACTAAAAAGAAACA 59.826 33.333 0.00 0.00 0.00 2.83
2174 2484 7.693951 CCTCATATGCGAACTAAAAAGAAACAG 59.306 37.037 0.00 0.00 0.00 3.16
2175 2485 7.526608 TCATATGCGAACTAAAAAGAAACAGG 58.473 34.615 0.00 0.00 0.00 4.00
2176 2486 7.389330 TCATATGCGAACTAAAAAGAAACAGGA 59.611 33.333 0.00 0.00 0.00 3.86
2177 2487 5.418310 TGCGAACTAAAAAGAAACAGGAG 57.582 39.130 0.00 0.00 0.00 3.69
2178 2488 4.274950 TGCGAACTAAAAAGAAACAGGAGG 59.725 41.667 0.00 0.00 0.00 4.30
2179 2489 4.320275 GCGAACTAAAAAGAAACAGGAGGG 60.320 45.833 0.00 0.00 0.00 4.30
2180 2490 5.061179 CGAACTAAAAAGAAACAGGAGGGA 58.939 41.667 0.00 0.00 0.00 4.20
2181 2491 5.179555 CGAACTAAAAAGAAACAGGAGGGAG 59.820 44.000 0.00 0.00 0.00 4.30
2182 2492 5.648330 ACTAAAAAGAAACAGGAGGGAGT 57.352 39.130 0.00 0.00 0.00 3.85
2183 2493 6.758806 ACTAAAAAGAAACAGGAGGGAGTA 57.241 37.500 0.00 0.00 0.00 2.59
2184 2494 6.531923 ACTAAAAAGAAACAGGAGGGAGTAC 58.468 40.000 0.00 0.00 0.00 2.73
2185 2495 5.648330 AAAAAGAAACAGGAGGGAGTACT 57.352 39.130 0.00 0.00 0.00 2.73
2186 2496 5.648330 AAAAGAAACAGGAGGGAGTACTT 57.352 39.130 0.00 0.00 0.00 2.24
2187 2497 6.758806 AAAAGAAACAGGAGGGAGTACTTA 57.241 37.500 0.00 0.00 0.00 2.24
2188 2498 6.758806 AAAGAAACAGGAGGGAGTACTTAA 57.241 37.500 0.00 0.00 0.00 1.85
2189 2499 6.758806 AAGAAACAGGAGGGAGTACTTAAA 57.241 37.500 0.00 0.00 0.00 1.52
2225 2535 8.725148 ACTCAGACATTTCTCAACACAATATTC 58.275 33.333 0.00 0.00 0.00 1.75
2226 2536 8.620116 TCAGACATTTCTCAACACAATATTCA 57.380 30.769 0.00 0.00 0.00 2.57
2243 2566 7.013655 ACAATATTCAACCTGTCTCCATTATGC 59.986 37.037 0.00 0.00 0.00 3.14
2249 2572 3.118482 ACCTGTCTCCATTATGCAGTCTG 60.118 47.826 0.00 0.00 0.00 3.51
2256 2579 4.454678 TCCATTATGCAGTCTGGACAATC 58.545 43.478 9.24 0.00 32.92 2.67
2290 2613 6.260271 CGGGAAGGTATTTGAGAGGAAATAAC 59.740 42.308 0.00 0.00 36.23 1.89
2328 2651 3.135994 AGTAGTTGGGTTTACTTGCACG 58.864 45.455 0.00 0.00 0.00 5.34
2344 2667 6.170506 ACTTGCACGATAAATCTCCAACTTA 58.829 36.000 0.00 0.00 0.00 2.24
2346 2669 7.336931 ACTTGCACGATAAATCTCCAACTTATT 59.663 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 226 7.040201 CCTGGAAGAGAAAACATTGAGATCAAA 60.040 37.037 0.00 0.00 36.01 2.69
396 397 7.532571 ACTGTCATTTCACATATCACACATTG 58.467 34.615 0.00 0.00 0.00 2.82
512 513 7.565768 ACACTTTTAAGGGTTGAAAAATAGGGA 59.434 33.333 0.00 0.00 40.45 4.20
517 518 9.508642 TTTTGACACTTTTAAGGGTTGAAAAAT 57.491 25.926 0.00 0.00 44.15 1.82
660 661 3.510360 CCTTCGGTCTCAAAGGAACTAGA 59.490 47.826 0.00 0.00 44.02 2.43
709 711 2.556840 TAATGCAGCCCTGGCAGACC 62.557 60.000 17.94 6.15 45.68 3.85
816 839 3.244976 GTGCTAATTGAATTGCGCTTGT 58.755 40.909 9.73 0.00 33.71 3.16
844 871 4.065281 ACCCTGACGTACAGCCGC 62.065 66.667 8.85 0.00 44.52 6.53
894 921 3.033764 GCACGAACGGCGAAGTGA 61.034 61.111 27.21 0.00 44.57 3.41
895 922 3.000080 GAGCACGAACGGCGAAGTG 62.000 63.158 16.62 20.24 44.57 3.16
896 923 2.733593 GAGCACGAACGGCGAAGT 60.734 61.111 16.62 7.43 44.57 3.01
907 934 2.159382 AGTTAAATTGTGGGGAGCACG 58.841 47.619 0.00 0.00 0.00 5.34
1388 1491 1.675552 CGAAATAAGGGGTTGCGGAT 58.324 50.000 0.00 0.00 0.00 4.18
1395 1498 2.914941 ACCTACAACCGAAATAAGGGGT 59.085 45.455 0.00 0.00 34.99 4.95
1423 1528 1.269166 CACGCAAAGTAGCTAGACCG 58.731 55.000 0.00 0.00 0.00 4.79
1445 1581 2.365582 ACACGAGCTTGAAACAAAGGT 58.634 42.857 8.31 0.00 40.47 3.50
1667 1820 2.613725 CGGGTAAGGAAACGCTTAACCT 60.614 50.000 11.37 0.00 39.93 3.50
1668 1821 1.733912 CGGGTAAGGAAACGCTTAACC 59.266 52.381 0.00 0.00 39.01 2.85
1669 1822 2.416747 ACGGGTAAGGAAACGCTTAAC 58.583 47.619 0.00 0.00 0.00 2.01
1671 1824 2.837532 AACGGGTAAGGAAACGCTTA 57.162 45.000 0.00 0.00 0.00 3.09
1672 1825 2.613725 CCTAACGGGTAAGGAAACGCTT 60.614 50.000 0.00 0.00 34.58 4.68
1673 1826 1.066645 CCTAACGGGTAAGGAAACGCT 60.067 52.381 0.00 0.00 34.58 5.07
1730 1954 7.360946 GCAGTACTTTTCTATTCGGTGTTGATT 60.361 37.037 0.00 0.00 0.00 2.57
1731 1955 6.092259 GCAGTACTTTTCTATTCGGTGTTGAT 59.908 38.462 0.00 0.00 0.00 2.57
1740 1964 5.361427 GGAGGAGGCAGTACTTTTCTATTC 58.639 45.833 0.00 0.00 0.00 1.75
1744 1968 1.550976 CGGAGGAGGCAGTACTTTTCT 59.449 52.381 0.00 0.00 0.00 2.52
1747 1971 1.349067 AACGGAGGAGGCAGTACTTT 58.651 50.000 0.00 0.00 0.00 2.66
1760 1987 1.359475 GTCGGCTAGCCTAACGGAG 59.641 63.158 30.55 13.82 0.00 4.63
1764 1991 1.718396 AAAACGTCGGCTAGCCTAAC 58.282 50.000 30.55 24.96 0.00 2.34
1827 2137 8.946085 GTGTATCCTTAGATTGACAATTTGACA 58.054 33.333 2.79 0.00 33.67 3.58
1844 2154 1.668826 TTGGGCCTCAGTGTATCCTT 58.331 50.000 4.53 0.00 0.00 3.36
1845 2155 1.898863 ATTGGGCCTCAGTGTATCCT 58.101 50.000 4.53 0.00 0.00 3.24
1846 2156 3.857157 TTATTGGGCCTCAGTGTATCC 57.143 47.619 4.53 0.00 0.00 2.59
1847 2157 6.076981 CAATTTATTGGGCCTCAGTGTATC 57.923 41.667 4.53 0.00 34.22 2.24
1870 2180 5.412286 GTCTCGGTAGTACTATCTCCATTCC 59.588 48.000 11.35 2.20 0.00 3.01
1871 2181 6.232692 AGTCTCGGTAGTACTATCTCCATTC 58.767 44.000 11.35 0.00 0.00 2.67
1890 2200 4.827284 TGGAGGTTCAAAAATTGGAGTCTC 59.173 41.667 0.00 0.00 0.00 3.36
1926 2236 3.188667 GCAGAGTAAAAAGAAACGGAGGG 59.811 47.826 0.00 0.00 0.00 4.30
1927 2237 3.813166 TGCAGAGTAAAAAGAAACGGAGG 59.187 43.478 0.00 0.00 0.00 4.30
1928 2238 5.613358 ATGCAGAGTAAAAAGAAACGGAG 57.387 39.130 0.00 0.00 0.00 4.63
1930 2240 8.879759 TCTTATATGCAGAGTAAAAAGAAACGG 58.120 33.333 0.00 0.00 0.00 4.44
1938 2248 9.679661 TGACCAAATCTTATATGCAGAGTAAAA 57.320 29.630 0.00 0.00 0.00 1.52
1939 2249 9.679661 TTGACCAAATCTTATATGCAGAGTAAA 57.320 29.630 0.00 0.00 0.00 2.01
1940 2250 9.679661 TTTGACCAAATCTTATATGCAGAGTAA 57.320 29.630 0.00 0.00 0.00 2.24
1941 2251 9.330063 CTTTGACCAAATCTTATATGCAGAGTA 57.670 33.333 0.00 0.00 0.00 2.59
1942 2252 7.831193 ACTTTGACCAAATCTTATATGCAGAGT 59.169 33.333 0.00 0.00 0.00 3.24
1943 2253 8.218338 ACTTTGACCAAATCTTATATGCAGAG 57.782 34.615 0.00 0.00 0.00 3.35
1944 2254 7.828717 TGACTTTGACCAAATCTTATATGCAGA 59.171 33.333 0.00 0.00 0.00 4.26
1945 2255 7.988737 TGACTTTGACCAAATCTTATATGCAG 58.011 34.615 0.00 0.00 0.00 4.41
1946 2256 7.936496 TGACTTTGACCAAATCTTATATGCA 57.064 32.000 0.00 0.00 0.00 3.96
1947 2257 9.076596 GTTTGACTTTGACCAAATCTTATATGC 57.923 33.333 0.00 0.00 35.14 3.14
1951 2261 9.349713 TGTAGTTTGACTTTGACCAAATCTTAT 57.650 29.630 0.00 0.00 35.14 1.73
1952 2262 8.617809 GTGTAGTTTGACTTTGACCAAATCTTA 58.382 33.333 0.00 0.00 35.14 2.10
1953 2263 7.122055 TGTGTAGTTTGACTTTGACCAAATCTT 59.878 33.333 0.00 0.00 35.14 2.40
1954 2264 6.601613 TGTGTAGTTTGACTTTGACCAAATCT 59.398 34.615 0.00 0.00 35.14 2.40
1955 2265 6.791303 TGTGTAGTTTGACTTTGACCAAATC 58.209 36.000 0.00 0.00 35.14 2.17
1956 2266 6.767524 TGTGTAGTTTGACTTTGACCAAAT 57.232 33.333 0.00 0.00 35.14 2.32
1957 2267 6.576662 TTGTGTAGTTTGACTTTGACCAAA 57.423 33.333 0.00 0.00 0.00 3.28
1958 2268 6.207810 ACTTTGTGTAGTTTGACTTTGACCAA 59.792 34.615 0.00 0.00 0.00 3.67
1959 2269 5.708230 ACTTTGTGTAGTTTGACTTTGACCA 59.292 36.000 0.00 0.00 0.00 4.02
1960 2270 6.190954 ACTTTGTGTAGTTTGACTTTGACC 57.809 37.500 0.00 0.00 0.00 4.02
1970 2280 8.840833 AAATTTGGTCAAACTTTGTGTAGTTT 57.159 26.923 1.44 0.00 46.42 2.66
2041 2351 7.188834 TCAGATGCATCATGAAACGTATTTTC 58.811 34.615 27.81 0.00 43.63 2.29
2042 2352 7.087409 TCAGATGCATCATGAAACGTATTTT 57.913 32.000 27.81 0.00 0.00 1.82
2043 2353 6.682423 TCAGATGCATCATGAAACGTATTT 57.318 33.333 27.81 0.00 0.00 1.40
2044 2354 6.872628 ATCAGATGCATCATGAAACGTATT 57.127 33.333 27.81 9.20 0.00 1.89
2045 2355 7.967890 TTATCAGATGCATCATGAAACGTAT 57.032 32.000 27.81 13.68 0.00 3.06
2046 2356 7.967890 ATTATCAGATGCATCATGAAACGTA 57.032 32.000 27.81 13.72 0.00 3.57
2047 2357 6.872628 ATTATCAGATGCATCATGAAACGT 57.127 33.333 27.81 14.55 0.00 3.99
2048 2358 9.274065 CAATATTATCAGATGCATCATGAAACG 57.726 33.333 27.81 7.61 0.00 3.60
2107 2417 9.780186 AGCTTTGTAGAGTTTGACTAACTTTAT 57.220 29.630 3.78 0.00 47.00 1.40
2108 2418 9.609346 AAGCTTTGTAGAGTTTGACTAACTTTA 57.391 29.630 3.78 0.37 47.00 1.85
2109 2419 8.398665 CAAGCTTTGTAGAGTTTGACTAACTTT 58.601 33.333 0.00 1.31 47.00 2.66
2110 2420 7.769044 TCAAGCTTTGTAGAGTTTGACTAACTT 59.231 33.333 0.00 0.00 47.00 2.66
2112 2422 7.478520 TCAAGCTTTGTAGAGTTTGACTAAC 57.521 36.000 0.00 0.00 40.46 2.34
2129 2439 3.365472 AGGTTTGGTCAAAGTCAAGCTT 58.635 40.909 0.00 0.00 39.52 3.74
2130 2440 2.952310 GAGGTTTGGTCAAAGTCAAGCT 59.048 45.455 0.00 0.00 0.00 3.74
2131 2441 2.687935 TGAGGTTTGGTCAAAGTCAAGC 59.312 45.455 0.00 0.00 0.00 4.01
2132 2442 6.615088 CATATGAGGTTTGGTCAAAGTCAAG 58.385 40.000 0.00 3.87 31.87 3.02
2133 2443 5.048083 GCATATGAGGTTTGGTCAAAGTCAA 60.048 40.000 6.97 0.00 31.87 3.18
2134 2444 4.458989 GCATATGAGGTTTGGTCAAAGTCA 59.541 41.667 6.97 9.49 32.34 3.41
2135 2445 4.437390 CGCATATGAGGTTTGGTCAAAGTC 60.437 45.833 6.97 0.00 0.00 3.01
2136 2446 3.440173 CGCATATGAGGTTTGGTCAAAGT 59.560 43.478 6.97 0.00 0.00 2.66
2137 2447 3.689161 TCGCATATGAGGTTTGGTCAAAG 59.311 43.478 6.97 0.00 0.00 2.77
2138 2448 3.680490 TCGCATATGAGGTTTGGTCAAA 58.320 40.909 6.97 0.00 0.00 2.69
2139 2449 3.342377 TCGCATATGAGGTTTGGTCAA 57.658 42.857 6.97 0.00 0.00 3.18
2140 2450 3.006940 GTTCGCATATGAGGTTTGGTCA 58.993 45.455 6.97 0.00 0.00 4.02
2141 2451 3.270877 AGTTCGCATATGAGGTTTGGTC 58.729 45.455 6.97 0.00 0.00 4.02
2142 2452 3.350219 AGTTCGCATATGAGGTTTGGT 57.650 42.857 6.97 0.00 0.00 3.67
2143 2453 5.811399 TTTAGTTCGCATATGAGGTTTGG 57.189 39.130 6.97 0.00 0.00 3.28
2144 2454 7.526608 TCTTTTTAGTTCGCATATGAGGTTTG 58.473 34.615 6.97 0.00 0.00 2.93
2145 2455 7.681939 TCTTTTTAGTTCGCATATGAGGTTT 57.318 32.000 6.97 0.00 0.00 3.27
2146 2456 7.681939 TTCTTTTTAGTTCGCATATGAGGTT 57.318 32.000 6.97 0.00 0.00 3.50
2147 2457 7.174253 TGTTTCTTTTTAGTTCGCATATGAGGT 59.826 33.333 6.97 0.00 0.00 3.85
2148 2458 7.526608 TGTTTCTTTTTAGTTCGCATATGAGG 58.473 34.615 6.97 0.00 0.00 3.86
2149 2459 7.693951 CCTGTTTCTTTTTAGTTCGCATATGAG 59.306 37.037 6.97 2.88 0.00 2.90
2150 2460 7.389330 TCCTGTTTCTTTTTAGTTCGCATATGA 59.611 33.333 6.97 0.00 0.00 2.15
2151 2461 7.526608 TCCTGTTTCTTTTTAGTTCGCATATG 58.473 34.615 0.00 0.00 0.00 1.78
2152 2462 7.148239 CCTCCTGTTTCTTTTTAGTTCGCATAT 60.148 37.037 0.00 0.00 0.00 1.78
2153 2463 6.148811 CCTCCTGTTTCTTTTTAGTTCGCATA 59.851 38.462 0.00 0.00 0.00 3.14
2154 2464 5.048713 CCTCCTGTTTCTTTTTAGTTCGCAT 60.049 40.000 0.00 0.00 0.00 4.73
2155 2465 4.274950 CCTCCTGTTTCTTTTTAGTTCGCA 59.725 41.667 0.00 0.00 0.00 5.10
2156 2466 4.320275 CCCTCCTGTTTCTTTTTAGTTCGC 60.320 45.833 0.00 0.00 0.00 4.70
2157 2467 5.061179 TCCCTCCTGTTTCTTTTTAGTTCG 58.939 41.667 0.00 0.00 0.00 3.95
2158 2468 6.062749 ACTCCCTCCTGTTTCTTTTTAGTTC 58.937 40.000 0.00 0.00 0.00 3.01
2159 2469 6.014771 ACTCCCTCCTGTTTCTTTTTAGTT 57.985 37.500 0.00 0.00 0.00 2.24
2160 2470 5.648330 ACTCCCTCCTGTTTCTTTTTAGT 57.352 39.130 0.00 0.00 0.00 2.24
2161 2471 6.770542 AGTACTCCCTCCTGTTTCTTTTTAG 58.229 40.000 0.00 0.00 0.00 1.85
2162 2472 6.758806 AGTACTCCCTCCTGTTTCTTTTTA 57.241 37.500 0.00 0.00 0.00 1.52
2163 2473 5.648330 AGTACTCCCTCCTGTTTCTTTTT 57.352 39.130 0.00 0.00 0.00 1.94
2164 2474 5.648330 AAGTACTCCCTCCTGTTTCTTTT 57.352 39.130 0.00 0.00 0.00 2.27
2165 2475 6.758806 TTAAGTACTCCCTCCTGTTTCTTT 57.241 37.500 0.00 0.00 0.00 2.52
2166 2476 6.758806 TTTAAGTACTCCCTCCTGTTTCTT 57.241 37.500 0.00 0.00 0.00 2.52
2167 2477 6.758806 TTTTAAGTACTCCCTCCTGTTTCT 57.241 37.500 0.00 0.00 0.00 2.52
2199 2509 8.627208 AATATTGTGTTGAGAAATGTCTGAGT 57.373 30.769 0.00 0.00 32.80 3.41
2243 2566 3.441572 GTCCCAATTGATTGTCCAGACTG 59.558 47.826 7.12 0.00 36.06 3.51
2249 2572 1.102978 CCCGTCCCAATTGATTGTCC 58.897 55.000 7.12 0.00 36.06 4.02
2256 2579 2.729028 ATACCTTCCCGTCCCAATTG 57.271 50.000 0.00 0.00 0.00 2.32
2290 2613 2.123511 TTGGCTGTGGTGTTGGGG 60.124 61.111 0.00 0.00 0.00 4.96


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.